STRAPS
STRAPS (STR'uctural '''A'nalysis of 'P'eptide 'S'econdary Structure) is a script written for the O'Mara Research Group at the Research School of Chemistry (Australian National University) to provide a visual representation of the results of the DSSP algorithm applied to a short peptide sequence. It is hoped that the use of the script will allow for the efficient production of informative data regarding the ensemble states of intrinsically-disordered peptides (IDPs). This is because, in contrast to large tertiary-state proteins, the interaction sites of IDPs are formed from short segments known as linear motifs, and an understanding of the statistical behaviour of these regions is thus of some importance for understanding the behaviours of IDPs. Further, by their nature, intrinsically-disordered peptides escape structural characterisation by usual experimental methods and will often assume many distinct (yet related) three-dimensional structures. The understanding of the dynamics and relative population of these distinct states is sometimes thus more important than the final structures themselves. '''Use of STRAPS STRAPS is used to generate plots of the frequency with which every residue of a simulated peptide assumes a particular secondary structural motif over the course of a trajectory, using the DSSP algorithm implementation developed by MDTraj . At the beginning of each time-step, a particular residue is assigned one of 9 (including non-protein) structure designations, determined by the energy of the region and the dihedral angles of the residue, among other considerations. The use of STRAPS requires three compulsory inputs. These are, a trajectory file (for example, .XTC), and the corresponding topology file (e.g. .GRO). Finally, for historical reasons, the desired protein index from which to begin a plot must be provided. Details and examples of the use of STRAPS are provided below. ' Tutorial: STRAPS' STRAPS can be run through a Python distribution (personally I prefer Canopy as this contains most required dependencies by default) from the Terminal. It was written to do so on OSX so proceed on Windows / Linux with caution. It's reliability on these systems is due to be tested but to my knowledge no part of the STRAPS program is OS-specific. The use of STRAPS requires Python 2.7.x and cannot be run using Python 3.x If your Python distribution is in your PATH, it is likely one can access the script by typing: python STRAPS.py **** Note: This tutorial is in the process of being re-written and should be disregarded until a future date. **** 'Known Issues' The following section contains known errors or issues that may arise during the standard use of STRAPS, along with their solutions (if known). *'Segmentation Fault 11' This error will cause STRAPS to crash, and has been known to occur when the calculation of the DSSP assignments is too large for your computer hardware. For example, on the O'Mara group computer, I have encountered several SF11s when attempting to calculate the DSSP assignments for a system of ~850 residues in a 300ns trajectory (6000 frames). Working Solution: '''At this stage if one encounters this error, you can choose to use trjconv to skip every, say, fifth frame of your trajectory in the hope that this will sufficiently decrease the size of the trajectory. This is relatively fast and does not prevent one from sampling sufficient conformational space. *"The STRAPS plot just returned a black box!"' ''''There are two reasons for this error. Firstly, you may be attempting to plot the DSSP results for a sequence that is much too large to be succintly presented in a single figure. For example, I feel as though substantial clarity is lost for a sequence of 75 residues. In this case, the plotted result is in fact correct, but is so confined by the contraints of the figure size that only the edges of each bar in the bar plot can be seen. '''Working solution: '''You will need to consider whether the use of STRAPS for this system is appropriate. The second cause of this error is an extension of the first. If you have duplicates in your system (e.g. you are simulating multiple identical copies of a peptide), but each peptide copy only contains for example 30 residues, and you wish to visualise the structural behaviour of this system of 30 peptides, this can be done, but if you obtain a "black box" as your output you will need to consider the use of the de-duplicator flag (-d). '''Working solution: '''STRAPS has a de-duplicator flag (-d) exactly for these circumstances. Further details can be obtained in the tutorial above, or in the help module of STRAPS (-h). Obtaining STRAPS To obtain the script (free for any use), it has been placed on the shared drive in the SCRIPTS directory. Alternatively, contact Mitch or any other member of the O'Mara group who will probably know where to find a working copy, or will know how to contact me. Category:Guides